Refactor graph tests

- use pytest functions which can use fixtures
- use fixtures to reduce network roundtrips
- use parametrized fixture to control igraph usage
  - also splits igraph tests into 2

Author: clbarnes

pymaid/tests/conftest.py

@@ -0,0 +1,63 @@
+import os
+import pytest
+import navis
+from contextlib import contextmanager
+import logging
+import pymaid
+
+logger = logging.getLogger(__name__)
+
+
+@contextmanager
+def igraph_context(use_igraph):
+    orig = navis.config.use_igraph
+    logger.debug(f"Setting navis.config.use_igraph = {use_igraph}")
+    navis.config.use_igraph = use_igraph
+    yield use_igraph
+    logger.debug(f"Resetting navis.config.use_igraph = {orig}")
+    navis.config.use_igraph = orig
+
+
+@pytest.fixture(scope="session", params=[True, False])
+def use_igraph(request):
+    with igraph_context(request.param) as use:
+        yield use
+
+
+@pytest.fixture(scope="module")
+def client():
+    return pymaid.CatmaidInstance(
+        os.environ.get("PYMAID_TEST_SERVER_URL", 'https://fafb.catmaid.virtualflybrain.org/'),
+        os.environ.get("PYMAID_TEST_TOKEN"),
+        os.environ.get("PYMAID_TEST_HTTP_USER"),
+        os.environ.get("PYMAID_TEST_HTTP_PW"),
+        make_global=True,
+    )
+
+
+@pytest.fixture(scope="module")
+def skids():
+    return [
+        int(s) for s in os.environ.get(
+            "PYMAID_TEST_SKIDS",
+            "16,1299740,4744251"
+        ).split(",")
+    ]
+
+
+@pytest.fixture(scope="module")
+def annotation_names():
+    return os.environ.get(
+        "PYMAID_TEST_ANNOTATIONS",
+        'Paper: Dolan and Belliart-Guérin et al. 2018,Paper: Wang et al 2020a'
+    ).split(",")
+
+
+@pytest.fixture(scope="module")
+def volume_name():
+    return os.environ.get("PYMAID_TEST_VOLUME", "LH_R")
+
+
+@pytest.fixture(scope="module")
+def stack_id():
+    return int(os.environ.get("PYMAID_TEST_STACK_ID", 1))

pymaid/tests/test_graph.py

@@ -0,0 +1,81 @@
+import pytest
+import pymaid
+import navis as ns
+import numpy as np
+
+SEED = 1991
+
+@pytest.fixture(scope="module")
+def neuron_list(client, skids):
+    return pymaid.get_neuron(skids[0:2], remote_instance=client)
+
+
+@pytest.fixture(scope="module")
+def neuron(neuron_list):
+    n = neuron_list[0]
+    return n.reroot(n.soma, inplace=False)
+
+@pytest.fixture(scope="module")
+def leaf_slab(neuron):
+    rng = np.random.default_rng(SEED)
+    leaf_id = neuron.nodes[neuron.nodes.type == 'end'].sample(
+        1, random_state=rng).iloc[0].node_id
+    slab_id = neuron.nodes[neuron.nodes.type == 'slab'].sample(
+        1, random_state=rng).iloc[0].node_id
+    return (leaf_id, slab_id)
+
+
+def test_reroot(neuron_list, neuron, leaf_slab, use_igraph):
+    leaf_id, slab_id = leaf_slab
+    assert neuron.reroot(leaf_id, inplace=False) is not None
+    assert neuron_list.reroot(neuron_list.soma, inplace=False) is not None
+
+
+def test_distal_to(neuron, leaf_slab, use_igraph):
+    leaf_id, slab_id = leaf_slab
+    assert ns.distal_to(neuron, leaf_id, neuron.root)
+    assert not ns.distal_to(neuron, neuron.root, leaf_id)
+
+
+def test_distance(neuron, use_igraph):
+    leaf_id = neuron.nodes[neuron.nodes.type == 'end'].iloc[0].node_id
+
+    assert ns.dist_between(neuron, leaf_id, neuron.root) is not None
+    assert ns.dist_between(neuron, neuron.root, leaf_id) is not None
+
+
+def test_find_bp(neuron, use_igraph):
+    assert ns.find_main_branchpoint(neuron, reroot_soma=False) is not None
+
+
+def test_split_fragments(neuron, use_igraph):
+    assert ns.split_into_fragments(neuron, n=2, reroot_soma=False) is not None
+
+
+def test_longest_neurite(neuron, use_igraph):
+    assert ns.longest_neurite(neuron, n=2, reroot_soma=False) is not None
+
+
+def test_cut_neuron(neuron, leaf_slab, use_igraph):
+    leaf_id, slab_id = leaf_slab
+    dist, prox = ns.cut_skeleton(neuron, slab_id)
+    assert dist.nodes.shape != prox.nodes.shape
+
+    # Make sure dist and prox check out
+    assert ns.distal_to(neuron, dist.root, prox.root)
+
+
+def test_subset(neuron, use_igraph):
+    assert isinstance(
+        ns.subset_neuron(neuron, neuron.segments[0]),
+        pymaid.CatmaidNeuron
+    )
+
+
+def test_node_sorting(neuron, use_igraph):
+    result = ns.graph.node_label_sorting(neuron)
+    assert isinstance(result, np.ndarray)
+
+
+def test_geodesic_matrix(neuron, use_igraph):
+    geo = ns.geodesic_matrix(neuron)

pymaid/tests/test_pymaid.py

@@ -35,6 +35,7 @@
 import warnings
 import os
 import matplotlib as mpl
+import pytest
 #if os.environ.get('DISPLAY', '') == '':
 #    warnings.warn('No display found. Using template backend (nothing '
 #                  'will show).')
@@ -605,104 +606,6 @@ def test_guess_radius(self):
                               pymaid.CatmaidNeuron)
 
 
-class TestGraphs(unittest.TestCase):
-    """Test graph functions."""
-
-    def try_conditions(func):
-        """Runs each test under various conditions and asserts that results
-        are always the same."""
-
-        def wrapper(self, *args, **kwargs):
-            ns.config.use_igraph = False
-            res1 = func(self, *args, **kwargs)
-            if igraph:
-                ns.config.use_igraph = True
-                res2 = func(self, *args, **kwargs)
-                self.assertEqual(res1, res2)
-            return res1
-        return wrapper
-
-    def setUp(self):
-        self.rm = pymaid.CatmaidInstance(server=config_test.server_url,
-                                         http_user=config_test.http_user,
-                                         http_password=config_test.http_pw,
-                                         api_token=config_test.token,
-                                         make_global=True)
-
-        self.nl = pymaid.get_neuron(config_test.test_skids[0:2],
-                                    remote_instance=self.rm)
-
-        self.n = self.nl[0]
-        self.n.reroot(self.n.soma)
-
-        # Get some random leaf node
-        self.leaf_id = self.n.nodes[self.n.nodes.type == 'end'].sample(
-            1).iloc[0].node_id
-        self.slab_id = self.n.nodes[self.n.nodes.type == 'slab'].sample(
-            1).iloc[0].node_id
-
-    @try_conditions
-    def test_reroot(self):
-        self.assertIsNotNone(self.n.reroot(self.leaf_id, inplace=False))
-        self.assertIsNotNone(self.nl.reroot(self.nl.soma, inplace=False))
-
-    @try_conditions
-    def test_distal_to(self):
-        self.assertTrue(ns.distal_to(self.n, self.leaf_id, self.n.root))
-        self.assertFalse(ns.distal_to(self.n, self.n.root, self.leaf_id))
-
-    @try_conditions
-    def test_distance(self):
-        leaf_id = self.n.nodes[self.n.nodes.type == 'end'].iloc[0].node_id
-
-        self.assertIsNotNone(ns.dist_between(self.n,
-                                             leaf_id,
-                                             self.n.root))
-        self.assertIsNotNone(ns.dist_between(self.n,
-                                             self.n.root,
-                                             leaf_id))
-
-    @try_conditions
-    def test_find_bp(self):
-        self.assertIsNotNone(ns.find_main_branchpoint(self.n,
-                                                      reroot_soma=False))
-
-    @try_conditions
-    def test_split_fragments(self):
-        self.assertIsNotNone(ns.split_into_fragments(self.n,
-                                                     n=2,
-                                                     reroot_soma=False))
-
-    @try_conditions
-    def test_longest_neurite(self):
-        self.assertIsNotNone(ns.longest_neurite(self.n,
-                                                n=2,
-                                                reroot_soma=False))
-
-    @try_conditions
-    def test_cut_neuron(self):
-        dist, prox = ns.cut_skeleton(self.n, self.slab_id)
-        self.assertNotEqual(dist.nodes.shape, prox.nodes.shape)
-
-        # Make sure dist and prox check out
-        self.assertTrue(ns.distal_to(self.n, dist.root, prox.root))
-
-    @try_conditions
-    def test_subset(self):
-        self.assertIsInstance(ns.subset_neuron(self.n,
-                                               self.n.segments[0]),
-                              pymaid.CatmaidNeuron)
-
-    @try_conditions
-    def test_node_sorting(self):
-        self.assertIsInstance(ns.graph.node_label_sorting(self.n),
-                              list)
-
-    @try_conditions
-    def test_geodesic_matrix(self):
-        geo = ns.geodesic_matrix(self.n)
-
-
 class TestConnectivity(unittest.TestCase):
     """Test connectivity-related functions."""